Mercurial > repos > iuc > hal_halstats
changeset 1:a9eb29f924e1 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/haltools commit f46096b336bf460424143fc9d633b5e7c20bf1cf
| author | iuc |
|---|---|
| date | Thu, 05 Mar 2026 11:30:42 +0000 |
| parents | a9c52b2edba7 |
| children | |
| files | hal_halStats.xml macros.xml |
| diffstat | 2 files changed, 12 insertions(+), 12 deletions(-) [+] |
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--- a/hal_halStats.xml Fri Feb 06 10:48:53 2026 +0000 +++ b/hal_halStats.xml Thu Mar 05 11:30:42 2026 +0000 @@ -7,11 +7,11 @@ <expand macro="stdio"/> <command detect_errors="aggressive"><![CDATA[ set -o pipefail; ## Sets the pipeline’s exit code to halStats’s on failure. - ( ## echo headers for specific numerical data + ## echo headers for specific numerical data #if $mode.option == '--baseComp': - echo -e 'fraction_of_As\tfraction_of_Gs\tfraction_of_Cs\tfraction_of_Ts'; + echo -e 'fraction_of_As\tfraction_of_Gs\tfraction_of_Cs\tfraction_of_Ts' >> '$out_file' && #else if $mode.option == '--numSegments': - echo -e 'numTopSegments\tnumBottomSegments'; + echo -e 'numTopSegments\tnumBottomSegments' >> '$out_file' && #end if halStats #if $mode.option == '--allCoverage': @@ -60,13 +60,13 @@ --topSegments '$mode.topSegments' #end if '$input_hal' - ## Pipes specific output to replace commas with tabs. Output is mostly numerical, and Genome names contain no commas, as this would invalidate the HAL Newick tree. - #if $mode.option == '--allCoverage' or $mode.option == '--sequenceStats' or $mode.option == '--percentID' or $mode.option == '--coverage': - | tr ',' '\t' - #else if $mode.option == '--numSegments': - | tr ' ' '\t' ## Replace spaces - #end if - ) > '$out_file' + ## Pipes specific output to replace commas with tabs. Output is mostly numerical, and Genome names contain no commas, as this would invalidate the HAL Newick tree. + #if $mode.option == '--allCoverage' or $mode.option == '--sequenceStats' or $mode.option == '--percentID' or $mode.option == '--coverage': + | tr ',' '\t' + #else if $mode.option == '--numSegments': + | tr ' ' '\t' ## Replace spaces + #end if + >> '$out_file' ]]></command> <inputs> <expand macro="input_hal"/>
--- a/macros.xml Fri Feb 06 10:48:53 2026 +0000 +++ b/macros.xml Thu Mar 05 11:30:42 2026 +0000 @@ -5,7 +5,7 @@ </requirements> </xml> <token name="@TOOL_VERSION@">2.9.9</token> - <token name="@VERSION_SUFFIX@">0</token> + <token name="@VERSION_SUFFIX@">1</token> <token name="@PROFILE@">25.1</token> <xml name="stdio"> <stdio> @@ -171,7 +171,7 @@ <validator type="regex" message="Enter without leading or trailing spaces">^\S(?:.*\S)?$</validator> </xml> <xml name="validator_comma_list"> - <validator type="regex" message="Enter a comma separated list of genomes, without leading or trailing spaces">^\S(?:[^,]*\S)?(?:,\S(?:[^,]*\S)?)*$</validator> + <validator type="regex" message="Enter a comma separated list of genomes, without leading or trailing spaces">^[^,\s]+(,[^,\s]+)*$</validator> </xml> <xml name="validator_newick"> <validator type="regex" message="Enter a Newick tree">^.*;$</validator>